USH2A c.784+162del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 6.11%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +162 | deep intronic (+162 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.85 | GERP -1.6 |
| Non-coding constraint | Z 0.52 | 1 kb window · o/e 0.96 · regional · uncalibrated |
| Overall | ||
| CADD | 1.874 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.11%
African / African-American · 2,540/41,550 alleles
Filtering AF
5.91%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.83%
Overall
1.82%
2,772/152,298 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.11% | 16 |
| Admixed American | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 1.09% | 92 |
| South Asian | 0.0414% | 2,415 |
| European (non-Finnish) | 0.0176% | 5,668 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- USH2A
- Coding
- c.784+162del
- MANE Select
- NM_206933
- dbSNP
- rs67328101
- Type
- Deletion
- Location
- chr1:216364791 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Similar variants
- USH2A c.12295-?_14133+?del Likely pathogenic ★★★ same type
- USH2A c.11389+1del Pathogenic/Likely pathogenic ★★ same type
- USH2A c.11549del Pathogenic/Likely pathogenic ★★ same type
- USH2A c.4251+1del Pathogenic/Likely pathogenic ★★ same type
- USH2A c.4758+1del Pathogenic/Likely pathogenic ★★ same type
- USH2A c.486-4_486-2del Likely pathogenic ★★ same type
- USH2A c.7594+2del Likely pathogenic ★★ same type
- USH2A c.9055+1del Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ush2a-c-784-plus-162del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown